Quantifying histogram data

What is the best method to quantify your data from flow cytometry histograms?

As far as I looked, you can use the mean fluorescence intensity to compare two experimental conditions. However, this is not always a good strategy. For instance, in my ROS measurements I get small (unespecific) peaks of fluorescence behind the main peak, and this affects the mean fluorescence.

Another possibility is to create and quantify regions at the right and left of a certain point. However, I never know how to decide where should be this reference point...